X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=b5ed0521c9f46785e4054e1571d73b2329ef30c6;hb=8b5145f0837eeaeb1f029de179a3715a174dfa09;hp=00fcb9c39c598d12dc6d285b5b9720bb080ba129;hpb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 00fcb9c..b5ed052 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -20,6 +20,10 @@
  */
 package jalview.io;
 
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.List;
 import java.util.Locale;
 
 import jalview.api.AlignExportSettingsI;
@@ -34,11 +38,6 @@ import jalview.ext.jmol.JmolParser;
 import jalview.structure.StructureImportSettings;
 import jalview.util.Platform;
 
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.List;
-
 /**
  * A low level class for alignment and feature IO with alignment formatting
  * methods used by both applet and application for generating flat alignment
@@ -159,6 +158,13 @@ public class AppletFormatAdapter
           DataSourceType sourceType, FileFormatI fileFormat)
           throws IOException
   {
+    return readFile(selectedFile, file, sourceType, fileFormat, null);
+  }
+
+  public AlignmentI readFile(File selectedFile, String file,
+          DataSourceType sourceType, FileFormatI fileFormat,
+          StructureImportSettings.TFType tempfacType) throws IOException
+  {
 
     this.selectedFile = selectedFile;
     if (selectedFile != null)
@@ -177,11 +183,16 @@ public class AppletFormatAdapter
                         .toString());
         StructureImportSettings.addSettings(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct);
+        if (tempfacType != null)
+        {
+          StructureImportSettings.setTemperatureFactorType(tempfacType);
+        }
         if (isParseWithJMOL)
         {
           // needs a File option
           alignFile = new JmolParser(
-                  selectedFile == null ? inFile : selectedFile, sourceType);
+                  selectedFile == null ? inFile : selectedFile, sourceType,
+                  StructureImportSettings.getTemperatureFactorType());
         }
         else
         {